FIMO version 4.10.0, (Release date: Wed May 21 10:35:36 2014 +1000)

For further information on how to interpret these results or to get a copy of the FIMO software please access http://meme.nbcr.net

If you use FIMO in your research, please cite the following paper:
Charles E. Grant, Timothy L. Bailey, and William Stafford Noble, "FIMO: Scanning for occurrences of a given motif", Bioinformatics, 27(7):1017-1018, 2011. [full text]

• There were 148 motif occurrences with a p-value less than 0.0001.
• The p-value of a motif occurrence is defined as the probability of a random sequence of the same length as the motif matching that position of the sequence with as good or better a score.
• The score for the match of a position in a sequence to a motif is computed by summing the appropriate entries from each column of the position-dependent scoring matrix that represents the motif.
• The q-value of a motif occurrence is defined as the false discovery rate if the occurrence is accepted as significant.
• The table is sorted by increasing p-value.

Command line:

/share/pkg/meme/4.10.0_4/install/bin/fimo --parse-genomic-coord --verbosity 1 --oc Dynamic_Male-biased_Output/fimo_out_3 --bgfile Dynamic_Male-biased_Output/background --motif RATCAATA Dynamic_Male-biased_Output/dreme_out/dreme.xml Dynamic_Male-biased_Output/Dynamic_Male-biased.fa

Settings:

output directory = Dynamic_Male-biased_Output/fimo_out_3
MEME file name = Dynamic_Male-biased_Output/dreme_out/dreme.xml
sequence file name = Dynamic_Male-biased_Output/Dynamic_Male-biased.fa


background file name = Dynamic_Male-biased_Output/background
allow clobber = true
compute q-values = true


parse genomic coord. = true
text only = false
scan both strands = true


max sequence length = 250000000
output threshold = 0.0001
threshold type = p-value


max stored scores = 100000
pseudocount = 0.1
verbosity = 1


selected motif = RATCAATA

This information can be useful in the event you wish to report a problem with the FIMO software.